A tool to visualize the genomic neighbourhoods and phylogeny of anti-CRISPR and anti-CRISPR associated genes.
Running create_clinker_out.sh will generate everything except co_occurrence data and clinker plots, those must be generated separately. A description on how to generate clinker plots is found in create_clinker_out.sh.
The following scripts contain hard-coded directories and will need to be modified, or the directory hierarchy that the scripts were designed on will need to be mimicked. I may have missed some of the hard-coded paths, so if you get an error, that is likely the cause.
Scripts with hard-coded paths: co_occurrences.py create_clinker_out.sh db_phylogeny.py get_list_of_new_ncbi_bacterial_genomes_na.py get_list_of_new_ncbi_bacterial_genomes.py parse_genbank_file.py parse_psiblast_out.py run_psiblasts.sh set_directories_matches.sh update_ncbi_bacterial_genomes.sh
Original File Hierarchy (the files provided make up the contents of /birl2/data/Acr/clean/scripts/ ):
/birl2/data/Acr
/clean/
cooccurrences/
directory_of_genbank_matches_bacterial/
fastagenes/
psiblast_out/
scripts/
basictree.py
build_phylo.py
clinker/
all_match_names.txt
align.py
classes.py
disjoint_set/
examples/
formatters.py
__init__.py
main.py
plot/
clinker.js
clustermap.min.js
d3.min.js
index.html
mock.json
style.css
plot.py
co_occurrences.py
create_clinker_out.sh
db_phylogeny.py
get_list_of_new_ncbi_bacterial_genomes_na.py
get_list_of_new_ncbi_bacterial_genomes.py
parse_genbank_file.py
parse_psiblast_out.py
phylo_pipe.sh
run_cooccurrences.sh
run_find_genomes.sh
run_psiblasts.sh
set_directories_matches.sh
split_pal.py
split_query_name.py
update_ncbi_bacterial_genomes.sh
tabdelimitedouts_bacterial/
/data
/updateddb
all_pal_names.txt
db_volume_files.....
/bacterial_genomes
/gbff
all.gbff
files.gbff
in.gbff
the.gbff
database.gbff
Uses modified code from Clinker: clinker & clustermap.js: Automatic generation of gene cluster comparison figures. Gilchrist, C.L.M., Chooi, Y.-H., 2020. Bioinformatics. doi: https://doi.org/10.1093/bioinformatics/btab007
The python library disjoint-set will need to be installed for clinker to run properly. This can be done from the command line with: pip install disjoint-set